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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings NestLink_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-data-experiment/meat/NestLink.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-26 16:44:31 UTC
* checking for file ‘NestLink/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NestLink’ version ‘1.27.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'AnnotationHub', 'ExperimentHub', 'Biostrings', 'gplots', 'protViz',
  'ShortRead'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘NestLink’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with no role:
  Damien Morger <damien.morger@rqmicro.com>
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) runNGSAnalysis.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:35: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
runNGSAnalysis           138.670  2.243 141.244
getExperimentHubFilename  12.464  1.674  15.867
getFC                      5.134  0.357   5.699
WU160118                   3.772  0.732   5.206
NB.unique                  3.262  0.233  23.634
NB.unambiguous             3.188  0.287  23.612
F255744                    2.779  0.165  23.091
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-data-experiment/meat/NestLink.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL NestLink
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘NestLink’ ...
** this is package ‘NestLink’ version ‘1.27.0’
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NestLink)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #R
> 
> library(testthat)
> 
> suppressPackageStartupMessages(library(NestLink))
> 
> test_check("NestLink")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
 20.797   1.594  22.953